IMAP-WORKFLOWS

Snakemake workflows for microbiome and multi-omics data analysis

Fostering Reproducible Microbiome data Analysis with Snakemake workflow

Microbiome data analysis

…BRIEF INTRO IN PROGRESS…

IMAP-PART 01

Software requirement for microbiome data analysis

IMAP-PART 02

Exploring and profiling SRA sample metadata

IMAP-PART 03

Downloading SRA FastQ reads using fasterq-dump

IMAP-PART 04

Quality Control of Sequencing Reads

IMAP-PART 05

Microbial profiling with MOTHUR pipeline

IMAP-PART 06

Microbial profiling with QIIME2 pipeline

IMAP-PART 07

Microbial & functional profiling with BIOBAKERY pipelines

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Related work

Repo	Description	Status
IMAP-GLIMPSE	IMAP project overview	In-progress
IMAP-PART 01	Software requirement for microbiome data analysis with Snakemake workflows	In-progress
IMAP-PART 02	Downloading and exploring microbiome sample metadata from SRA Database	In-progress
IMAP-PART 03	Downloading and filtering microbiome sequencing data from SRA database	In-progress
IMAP-PART 04	Quality Control of Microbiome Next Generation Sequencing Reads	In-progress
IMAP-PART 05	Microbial profiling using MOTHUR pipeline with Snakemake workflows	In-progress
IMAP-PART 06	Microbial profiling using QIIME2 pipeline with Snakemake workflows	In-progress
IMAP-PART 07	Microbial & Functional profiling using BIOBAKERY pipelines with Snakemake workflows	In-progress
IMAP-SUMMARY	Summary of Snakemake workflows for microbiome data analysis	In-progress

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Multi-Omics data analysis

…BRIEF INTRO IN PROGRESS…

Citation

Please consider citing the iMAP article^[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.

References

[1]

Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4

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Appendix

Project main tree

.
├── LICENSE
├── README.md
├── config
│   └── config.yml
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── images
│   ├── bioinformatics.png
│   ├── bkgd.png
│   ├── imap.png
│   ├── imap_part01.svg
│   ├── imap_part02.svg
│   ├── imap_part03.svg
│   ├── imap_part04.svg
│   ├── imap_part05.svg
│   ├── imap_part06.svg
│   ├── imap_part07.svg
│   ├── rulegraph.png
│   └── smkreport
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── export.bib
│   ├── imap.bib
│   └── references.bib
├── report.html
├── results
│   └── project_tree.txt
├── smk.css
├── styles.css
└── workflow
    ├── Snakefile
    ├── envs
    │   ├── mothur.yml
    │   └── qiime220232.yml
    ├── report
    │   ├── biobakery.rst
    │   ├── imap.rst
    │   ├── mothur.rst
    │   ├── qiime2.rst
    │   ├── readqc.rst
    │   ├── rsmkrpt.rst
    │   ├── software.rst
    │   ├── sracache.rst
    │   ├── srametadata.rst
    │   ├── srareads.rst
    │   └── workflow.rst
    ├── rules
    │   ├── render_index.smk
    │   ├── report.smk
    │   └── rules_dag.smk
    └── scripts
        ├── README.md
        ├── files4smk_report.sh
        ├── render.R
        ├── rules_dag.sh
        ├── smk_html_report.sh
        └── tree.sh

12 directories, 48 files

Troubleshooting of FAQs

1. Question
Answer
2. Question
Answer

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Last updated on March 26, 2023.
Github_Repo: https://github.com/tmbuza/imap-snakemake-workflows.
Repo compiled and maintained by: Teresia Mrema-Buza.